MIT FOUNDATIONS IN COMPUTATIONAL AND

SYSTEMS BIOLOGY

Description
This course is an introduction to computational biology emphasizing the fundamentals of nucleic
acid and protein sequence and structural analysis; it also includes an introduction to the analysis
of complex biological systems. Topics covered in the course include principles and methods used
for sequence alignment, motif finding, structural modeling, structure prediction and network
modeling, as well as currently emerging research areas. This course is designed for advanced
undergraduates and graduate students with strong backgrounds in either molecular biology or
computer science, but not necessarily both. The scripting language Python—which is widely used
for bioinformatics and computational biology—will be used; foundational material covering basic
programming skills will be provided by the teaching assistants. Graduate versions of the course
involve an additional project component.

Textbook
This textbook is recommended for the course:
Zvelebil, Marketa J., and Jeremy O. Baum. Understanding Bioinformatics. Garland Science, 2007.
ISBN: 9780815340249. [Preview with Google books]
The instructors have also selected the following texts as particularly useful in specific areas, if you
are looking for more information:

Background in Python Programming

Ascher, David, and Mark Lutz. Learning Python. 2nd ed. O’Reilly Media, Inc., 2003. ISBN:
9780596002817. [Preview with Google Books]
Martelli, Alex. Python in a Nutshell. O’Reilly Media. 2006. ISBN: 9780596100469. [Preview with
Google Books]

Background in Molecular Biology, Cell Biology, and Biochemistry

Watson, James D., Tania A. Baker, et al. Molecular Biology of the Gene. Benjamin Cummings, 2013.
ISBN: 9780321762436.
Alberts, Bruce, Alexander Johnson, et al. Molecular Biology of the Cell. Garland Science, 2007.
ISBN: 9780815341055.
Berg, Jeremy M., John L. Tymoczko, et al. Biochemistry. W. H. Freeman, 2008. ISBN:
9781429235020.
Branden, Carl I., and John Tooze. Introduction to Protein Structure. Taylor & Francis, Inc., 2000.
Petsko, Gregory A., and Dagmar Ringe. Protein Structure and Function. Oxford University Press,
2008. ISBN: 9780199556847.

Other Useful References for the Class

Leach, Andrew. Molecular Modelling: Principles and Applications. Prentice Hall, 2001. ISBN:
9780582382107.
An in-depth treatment of molecular mechanics and other modeling methods.
Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and
Hall / CRC, 2013. ISBN: 9781439837177. [Preview with Google Books]
An introduction to topics related to biological networks from a physicist’s perspective.
Durbin, Richard, Sean R. Eddy, et al. Biological Sequence Analysis: Probabilistic Models of Proteins
and Nucleic Acids. Cambridge University Press, 1998. ISBN: 9780521629713.
Contains more in-depth discussion of many of the algorithms and methods discussed in class.
Glantz, Stanton. Primer of Biostatistics. McGraw-Hill Medical, 2011. ISBN: 9780071781503.
[Preview with Google Books]
Covers basic statistics with applications to biology and medicine.
Gonick, Larry, and Woollcott Smith. The Cartoon Guide to Statistics. Paw Prints, 2008. ISBN:
9781435242715.
A very useful introduction or refresher. Fun, but generally accurate.
Instructor Insights
Course Overview
This page focuses on the course 7.91J Foundations of Computational and Systems Biology as it was taught by
Profs. Christopher Burge, David Gifford, and Ernest Fraenkel in Spring 2014.
This course is an advanced undergraduate/graduate survey course in computational biology.
It is not a systems biology course, but topics important for analyzing complex systems will be presented.
It is not a synthetic biology course, but there is a guest lecture by George Church related to synthetic biology.
It is not an algorithms course; expertise in designing and analyzing algorithms is not assumed. The essential ideas
behind a variety of algorithms will be discussed, but details of implementation are not addressed. Students will
have the opportunity to implement at least one bioinformatics algorithm in the homework.

Course Outcomes
Course Goals for Students
To develop an understanding of foundational methods in computational biology
To enable students to contextualize and understand the basis of a good portion of the research literature in this
growing field
An additional goal for graduate students: to gain exposure to research in this field

Possibilities for Further Study/Careers

Graduate studies in computational biology
Careers in biotechnology

Curriculum Information
Prerequisites
Students should have a strong background in either molecular biology or computer science. Depending on which
course number the student enrolls in, there are different specific requirements.

Requirements Satisfied
None.

Offered
Every spring semester.

Assessment
The different versions of this course have different grading schemes. For example, this was the grading scheme
for graduate students in biology, biological engineering, and health sciences & technology:
30% Problem sets
48% Exams
20% Project
2% Project peer review

Student Information
Enrollment
64 students

Breakdown by Year
Juniors, seniors, and graduate students enrolled in this course.

Breakdown by Major
Students from biology, biological engineering, computer science, and health sciences & technology enrolled in
this course.

How Student Time Was Spent

During an average week, students were expected to spend 12 hours on the course, roughly divided as follows:

Lecture
Met two times per week for 1.5 hours per session; 26 sessions total.

Recitation
Met once a week for 1 hour per session. Optional attendance.

Out of Class
Work on assignments and the project.
Study for the exams.
Project
Students in one of the graduate versions of this course will complete a computational biology research project.
See the table for clarification.
The project is designed to give you practice in applying computational methods to contemporary problems in
biology. Students design and carry out projects working in a group or by themselves. There is grading
information below the steps of the project.

Steps of the Project

Interests
Teams
Specific Aims
Research Strategy
Written Report
Presentation
Peer Review
The due dates of the steps are listed on the calendar.

Interests
MIT students taking the course should email your background and interests to course staff. We will collate these
replies and post them on a private area of the course web site to help with team formation.

Teams
Submit a list of your team members, a title, and a one paragraph summary of the research problem you plan to
investigate. Groups can range in size from one student to five students. We suggest that you choose people to
work with who have skills complementary to yours.
For a one-paragraph summary of your project, you might look at these sample applications, especially the first
paragraph of specific aims pages. We encourage you to choose an area that is relevant to your current or planned
research. If you do not have data available to use for this project, a suitable publicly available dataset may be
found. Existing implementations of computational methods or custom programs may be used.

Specific Aims
Each team submits a one-page set of NIH grant-style specific aims that describe your project. Your aims should
correspond with goals you can reasonably achieve during the term. Your aims will be evaluated and returned with
comments to give you initial feedback on your formulation of your problem area.

Research Strategy
Each team submits a two-page (single spaced) research strategy describing the specific software that will be used
or developed, the specific data that will be analyzed, any relevant statistical methods, the sequence of research
activities and a brief comment on anticipated findings.

Written Report
Each team submits a five-page (single spaced) written report that summarizes your findings. (Figures are included
in the five-page limit, but references are not.) Each member of your group should author a clearly identified
section of the report with their specific contribution. This report will be graded as described below.
Your research strategy and results section should be structured to include the following sections, with the bulk of
the text in the Approach and Results section. (If you have multiple Specific Aims, then you may address
Significance, Innovation and Approach for each Specific Aim individually, or may address Significance, Innovation
and Approach for all of the Specific Aims collectively.)
Significance
Explain the importance of the problem or critical barrier to progress in the field that the proposed project
addresses.
Explain how the proposed project will improve scientific knowledge, technical capability, and/or clinical practice in
one or more broad fields.
Describe how the concepts, methods, technologies, treatments, services, or preventative interventions that drive
this field will be changed if the proposed aims are achieved.
Innovation
Explain how the work challenges and seeks to shift current research or clinical practice paradigms.
Describe any novel theoretical concepts, approaches or methodologies, instrumentation or interventions
developed or used, and any advantage over existing methodologies, instrumentation, or interventions.
Explain any refinements, improvements, or new applications of theoretical concepts, approaches or
methodologies, instrumentation, or interventions.
Approach and Results
Provide an introduction to the area, describing previous work.
Descibe the overall strategy, methodology, and analyses to be used to accomplish the specific aims of the project.
Include how the data was collected, analyzed, and interpreted.
Describe the results of your project in terms of your aim(s).
The page limit is to ensure that the report focuses on the key aspects of the problem method. Section (C) 1
should allow a colleague who is not expert in the specific research area to understand the report. Nevertheless, it
should take up no more than one page. Figures or tables may be helpful.
Formatting: Use 11 or 12 point font with at least one-inch margins, page numbers at the bottom, single spacing.